Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

(2015) Zhengting Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

(2015) Luciano A. Abriata et al.   PLoS One

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

(2014) Adrian WR Serohijos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Large pseudocounts andL2-norm penalties are necessary for the mean-field inference of Ising and Potts models

(2014) J. P. Barton et al.   PHYSICAL REVIEW E

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

The network of stabilizing contacts in proteins studied by coevolutionary data

(2013) Sara Lui et al.   JOURNAL OF CHEMICAL PHYSICS

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene

(2013) Martijn F. Schenk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Mutational effects on stability are largely conserved during protein evolution

(2013) O. Ashenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

(2012) T. Strunk et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution

(2012) Zhifeng Deng et al.   JOURNAL OF MOLECULAR BIOLOGY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks

(2011) Andrea Procaccini et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

The Role of a Second-Shell Residue in Modifying Substrate and Inhibitor Interactions in the SHV β-Lactamase: A Study of Ambler Position Asn276

(2009) Sarah M. Drawz et al.   BIOCHEMISTRY

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level

(2009) E. A. Franzosa et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

(2009) Jesse D. Bloom et al.   PLoS Computational Biology

Increased Folding Stability of TEM-1 β-Lactamase by In Vitro Selection

(2008) Insa Kather et al.   JOURNAL OF MOLECULAR BIOLOGY

SPROUTS: a database for the evaluation of protein stability upon point mutation

(2008) Mathieu Lonquety et al.   NUCLEIC ACIDS RESEARCH

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA